John Blischak 2014-05-14
Multiple users have observed that submitting jobs via Snakemake requires much more memory than is necessary to run the command (e.g. mailing list post, [Bitbucket issue][issue]).
Srividya Ramakrishnan srividya22
srividya22
/ README.md
Created
May 29, 2018 22:08
— forked from jdblischak/README.md
snakemake_vmem_usage
srividya22
/ README.md
Created
May 29, 2018 22:08
— forked from jdblischak/README.md
snakemake_vmem_usage
John Blischak 2014-05-14
Multiple users have observed that submitting jobs via Snakemake requires much more memory than is necessary to run the command (e.g. mailing list post, [Bitbucket issue][issue]).
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| Identify a directory which does not contain a particular file | |
| find base_dir -mindepth 2 -maxdepth 2 -type d '!' -exec test -e "{}/cover.jpg" ';' -print |
srividya22
/ BCFtools cheat sheet
Created
June 4, 2021 16:18
— forked from elowy01/BCFtools cheat sheet
BCFtools cheat sheet
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| *bcftools filter | |
| *Filter variants per region (in this example, print out only variants mapped to chr1 and chr2) | |
| qbcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz | |
| *printing out info for only 2 samples: | |
| bcftools view -s NA20818,NA20819 filename.vcf.gz | |
| *printing stats only for variants passing the filter: | |
| bcftools view -f PASS filename.vcf.gz |
srividya22
/ BCFtools cheat sheet
Created
June 4, 2021 16:18
— forked from elowy01/BCFtools cheat sheet
BCFtools cheat sheet
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| *bcftools filter | |
| *Filter variants per region (in this example, print out only variants mapped to chr1 and chr2) | |
| qbcftools filter -r1,2 ALL.chip.omni_broad_sanger_combined.20140818.snps.genotypes.hg38.vcf.gz | |
| *printing out info for only 2 samples: | |
| bcftools view -s NA20818,NA20819 filename.vcf.gz | |
| *printing stats only for variants passing the filter: | |
| bcftools view -f PASS filename.vcf.gz |
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